Beijing has removed Zhang Xiaoming from his position as director of the Hong Kong and Macau Affairs Office (HKMAO), demoting him to deputy director as part of a major shake-up.
Zhang's role as chief has been given to Xia Baolong, 68, a vice chairman of the Chinese People's Political Consultative Conference (CPPCC) and a former party secretary of Zhejiang province.
Zhang's demotion comes a little over a month after Wang Zhimin was sacked as the chief of Beijing's liaison office in Hong Kong, following the SAR's months of unrest.
Wang's replacement, Luo Huining, has now also been made a deputy director of the HKMAO, although he will keep his role as liaison office chief.
The director of the liaison office in Macau, Fu Ziying, has also been made a deputy director of the HKMAO, with the moves announced on Thursday in a brief statement from the central government.
Around two months into the extradition bill movement last year, Zhang and Wang held a closed-door seminar in Shenzhen for Hong Kong delegates to the National People's Congress, members of the CPPCC, and pro-establishment lawmakers.
Sources had said that Zhang warned that a "colour revolution" was taking place in the SAR, while Wang was quoted as saying the protests were due to a "development imbalance" in Hong Kong's capitalist society.
Analysts said Beijing had clearly been caught off guard by the months of protests and its officials had failed to read the pulse of the city.
New HKMAO chief Xia began his political career in Tianjian in the 1970s. He rose through the ranks and was promoted to deputy party chief of Zhejiang in 2003, becoming party secretary of the province in 2013.
Under his leadership in Zhejiang, some 2,000 crosses were torn down from churches across the province.